This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Variation in protein expression levels among individuals is thought to be an important source of physiological differences within and between species. However, relatively little is known about the magnitude and genetic basis of variation in protein expression levels. Recently, the Sanger Institute has resequenced the complete genomes of 37 Saccharomyces cerevisiae strains. This data set provides an important, novel, and powerful opportunity to synergistically combine comparative functional genomics data with comparative sequence analyses to delineate the genetic architecture of protein expression levels in yeast. Specifically, the goals of this project are two-fold. First, quantitative protein expression levels will be obtained for all 37 S. cerevisiae strains (or a maximally informative subset based upon their phylogenetic relationships), and protein levels that vary significantly among strains will be identified. Second, the whole genome sequence data will be leveraged to correlate patterns of protein expression levels with genetic variation. These data will provide the first systematic insight into the magnitude and patterns of natural protein expression variation as well as its genetic basis. This experiment represents a pilot experiment to first examine BY and RM strains.